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We agree that specific dissection of virus-infected cells marked by a GFP reporter could alleviate signal-to-noise problems. To achieve long-lasting overexpression of FoxP2, however, we used an AAV1 vector with a limited cloning capacity (~5 kb). In experiments not presented in this manuscript, viruses that expressed both FoxP2 and GFP separated by a P2A sequence, which reached 99.5% of the virus’s cloning capacity, yielded poor expression of the gene product and would have been useless for the behavioral experiments. In order to drive overexpression of FoxP2 to behaviorally relevant levels, our AAV1 vector had no tag on the FoxP2 transcript itself, making infected cells visually indistinguishable from uninfected cells.

Given that a single amino acid alteration in human FOXP2 leads to a severe speech and language disorder, we opted not to otherwise tag the zebra finch FoxP2 sequence that was inserted into the virus, avoiding any concern about altered function due to altered sequence. Another benefit of the construct was that it is the same as that used by Heston et al., (2015) enabling comparison and validation across studies.

What they did instead was group all the samples together (control and manipulated animals) and created a network expression analyses in Figure 3 , with the assumption that it is affected by the viral vector manipulations in Area X. One would hope that there is a partial affect from the 25% of cells of the manipulated Area X on the RNASeq data, and this can be tested. It took me some effort in re-reading to figure out what the authors did.

After reading the reviews, I see original reviewers 1and 2 had the same concern, just maybe not expressed as clearly. In response to that concern, the authors did a GFP manipulated Area X only analyses and came up with the same results ( Author response image 1 black cap flat in Brixton Brixton Brood UXwtZ0 of the response letter). This is good and should be included in the main paper.

As suggested, we have added the GFP-only network analysis to the main paper as ( Figure 3—figure supplement 1 ). Module preservation statistics indicate co-expression patterns that are distinct from the other construct-specific networks. This finding supports our claim of construct-specific gene co-expression.

However, they did not show network analyses of the viral FoxP2 manipulated animals, but instead show that clustering of expression does not differ between the GFP and FoxP2 manipulated Area X ( ASOS Washed DESIGN In Floral Mini Tall Tea Casual Dark Tall ASOS Print Dress z4Hzqwr of response letter). So, if we take their analyses at face value, this would mean that the combined network analyses of control and FoxP2 manipulated animals in Figure 3 of the manuscript may not be influenced by the FoxP2 manipulation, and instead is simply a control network similar to unmanipulated animals. This needs to be shown.

In addition to the GFP network, we now include individual network analyses for the FoxP2.FL and FoxP2.10+ groups. These are now included in the main paper as ( Figure 1—figure supplement 2 to Figure 1—figure supplement 5). The key findings are:

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then the parameter library will look for the file first in the subdirectory param/ of the local directory, then in your cxcds_param/ subdirectory of your home directory, and then finally fall back on the system default copy in the CIAO distribution (here taken to be /soft/ciao).

Setting the parameter file directory to the current working directory, e.g. "." (dot), is a special case. If you want to put the files in the current working directory, you must include a slash in the PFILES variable:

Each parameter is described by a comma-separated line of text listing the name, type, mode, value, minimum or enumeration, maximum, and prompt text for that parameter. See the table below for a description of these fields, and note that not all fields need to contain data. Blank lines and lines beginning with "#" are ignored.

As an example, consider the default parameter file for dmappend:

The infile and outfile parameters do not have any default value (the field is set to ""), and are listed as auto parameters (the "a" value) which is why plist does not include "()" around their names above. The verbose parameter defaults to 0 and is limited to be between 0 and 5, inclusive.

The acis_fef_lookup parameter contains an example of an enumerated list for the chipid parameter:

The |-separated list of items for the fifth field of the chipid parameter lists the valid values for this parameter. If a value other than none, NONE, or an integer between 0 and 9 is entered for the chipid parameter, then a warning message will be displayed and the user will be prompted for another value, as illustrated below.

Note that you can use the up and down arrows to cycle through the list of possible answers at the prompt.

In general this will occur when there's an "=" in the parameter value. For example:

The CXC parameter interface and related tools (pget, dmkeypar, etc) do not support an unsigned long datatype commonly used for engineering values. The values are stored as signed values so values greater than 2^31 are shown as negative values.

Uses SQL’s EXCEPT operator to keep only elements present in the QuerySet but not in some other QuerySet s. For example:

Returns a QuerySet that will “follow” foreign-key relationships, selecting additional related-object data when it executes its query. This is a performance booster which results in a single more complex query but means later use of foreign-key relationships won’t require database queries.

The following examples illustrate the difference between plain lookups and select_related() lookups. Here’s standard lookup:

And here’s select_related lookup:

You can use select_related() with any queryset of objects:

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The order of filter() and select_related() chaining isn’t important. These querysets are equivalent:

You can follow foreign keys in a similar way to querying them. If you have the following models:

… then a call to Book.objects.select_related('author__hometown').get(id=4) will cache the related Person and the related City :